## table of contents

primeDTLSR(1) | General Commands Manual | primeDTLSR(1) |

# NAME¶

primeDTLSR - Guest-in-host tree inference tool

# SYNOPSIS¶

**primeDTLSR** [*OPTIONS*]* seqfile hostfile
[**gsfile*]

# DESCRIPTION¶

Guest-in-host tree inference enabling reconciliation analysis using the underlying DTLRS model. Model properties:

- 1)
- The guest tree topology evolves inside the host tree by means of duplication, loss and horizontal transfer events guided by homogeneous rates, much like a birth-death process. Lineages branch deterministically at host tree nodes.
- 2)
- Relaxed molecular clock; sequence evolution rate variation over guest tree edges. Rates are drawn iid from specified distribution. Also, rate variation over sites may be added, using discretized gamma distribution with mean 1.
- 3)
- Substitution model of choice; standard or user-defined. The implementation uses a discretization of the host tree to approximate the probability of all possible reconciliation realizations for the current parameter state.

The implementation uses a discretization of the host tree to approximate the probability of all possible reconciliation realizations for the current parameter state.

*seqfile* is a file with aligned sequences for guest tree
leaves.

*hostfile* is a PrIME Newick file with host tree incl.
divergence times. Leaves must have time 0 and root have time > 0.

*gsfile* is a tab-delimited file relating guest tree leaves
to host tree leaves if info not included in *hostfile.*

# OPTIONS¶

**-h**,**-u**,**-?**- Display help (this text).
**-o***FILE*- Output filename. Defaults to stderr.
**-s***UNSIGNED_INT*- Seed for pseudo-random number generator. Defaults to random seed.
**-i***UNSIGNED_INT*- Number of iterations. Defaults to .
**-t***UNSIGNED_INT*- Thinning, i.e. sample every <value>-th iteration. Defaults to .
**-w***UNSIGNED_INT*- Output diagnostics to stderr every <value>-th sample. Defaults to .
**-q**- Do not output diagnostics. Non-quiet by default.
**-m****MCMC|PDHC|PD**- Execution type (MCMC, posterior density hill-climbing from initial values, or just initial posterior density). Defaults to .
**-Sm****UniformAA|JC69|JTT|UniformCodon|ArveCodon**- Substitution model. by default.
**-Su****DNA|AminoAcid|Codon**<Pi=float1 float2 ... floatn> <R=float1 float2 ...float(n*(n-1)/2)>- User-defined substitution model. The size of Pi and R must fit data type (DNA: n=4, AminoAcid: n=20, Codon: n=62). R is given as a flattened upper triangular matrix. Don't use both option -Su and -Sm.
**-Sn***UNSIGNED_INT*- Number of steps of discretized Gamma-distribution for sequence evolution rate variation over sites. Defaults to (no variation).
**-Ed****Gamma|InvG|LogN|Uniform**- Distribution for IID rate variation among edges. Defaults to .
**-Ep***FLOAT**FLOAT*-

Initial mean and variance of edge rate distribution. Defaults to and . **-Ef**- Fix mean and variance of edge rate distribution. Non-fixed by default.
**-Gi***FILE*- Filename with initial guest tree topology.
**-Gg**- Fix initial guest tree topology, i.e. perform no branch-swapping. Non-fixed by default.
**-Bp***FLOAT**FLOAT**FLOAT*- Initial duplication, loss and transfer rates. Defaults to , and .
**-Bf**- Fix duplication, loss and transfer rates to initial values. Non-fixed by default.
**-Bt***FLOAT*- Override time span of edge above root in host tree. Must be greater than 0. Defaults to file-contained value.
**-Dt***FLOAT*- Approximate discretization timestep. Set to 0 to divide edge generations into the same amount of parts (see -Di). Defaults to .
**-Di***UNSIGNED_INT*- Minimum number of discretization subintervals per edge generation. If -Dt is set 0, this becomes the exact number of subintervals. Minimum 2. @Defaults to conf_value_from_cmake_DiscMinIvs@.
**-C***UNSIGNED_INT*- Number of transfer counts during sampling. Defaults to .
**-r**- Rescale the host tree so that the root-to-leaf time equals 1.0. All inferred parameters will refer to the new scale. Off by default.
**-Z**- Do not print elapsed wall time and CPU time
**-W**- Do not print the command line
**-debuginfo**- Show misc. info to stderr before iterating. Not shown by default.

# EXIT STATUS¶

**0**- Successful program execution.
**1**- Some error occurred

# URL¶

# SEE ALSO¶

primeDLRS(1), primeGEM(1), showtree(1), chainsaw(1), reconcile(1), reroot(1), tree2leafnames(1), treesize(1)

13 Mar, 2012 | prime-phylo 1.0.11 |